- phenixbb - phenix-online.org

Phenix.Refine fix WXC has no effect
by White, Mark 17 Aug '20

17 Aug '20

Hello, I am refining a 3.5 Å structure using the latest stable version of Phenix.Refine. After switching to the latest version the Bond RMSDs exploded to ~ 0.035 Å, when using optimize wxc. Turning off Optimize and using the "Fix WXC" parameters in the GUI with increasingly smaller values had almost no effect on the final bond rmsds, which seems to explode from reasonable values in the "3_xyz" step of refinement. Am I missing something? Best regards, Mark Mark Andrew White, Ph.D. Associate Professor of Biochemistry & Molecular Biology, Manager, SCSB Macromolecular X-ray Laboratory UTMB, Galveston, TX http://xray.utmb.edu

4 4

Phenix.refine on coordinate-optimised structures
by Joey Farrell 07 Aug '20

07 Aug '20

Hello, I am trying to design a set of input parameters that I will be passing through the phenix.refine function. The structures that I am working with have already had their X,Y, and Z orthogonal Å coordinates optimised via separate protocol. I am looking for advice on which strategies and parameter values to use with phenix.refine to improve the crystallographic R-factors of such structures while preserving their earlier optimisation in real space. I have been having some success using “strategy = tls+individual_adp+occupancies” (where tls = “chain A”, tls = “chain B”, etc.) as well as adjusting the wxu_scale value until R-work and R-free are minimised. Are there other strategies or phenix.refine functionalities that may also prove helpful with this end in mind? I believe there may be ways to further improve R-work and R-free with this software that I am not yet aware of. Thank you for your help! Best, Joey

3 2

Phenix Real_Space_Refine and Torsion NCS restraints
by Mark A. White 04 Aug '20

04 Aug '20

Hello, Are there plans to include Torsion Angle NCS restraints in the Phenix.Real_Space_Refine module? At low resolution (~ 3-4Å) I would like to include NCS restraints, but my molecule is flexible and the strict NCS constraints used in the Real_Space_Refine module are not appropriate. I am currently using phenix-1.18.2-3874. Best regards, Mark

3 3

map to model - DNA model building
by Manoj saxena 04 Aug '20

04 Aug '20

Hello, I am trying to fit a cryo-EM map of a DNA protein complex (3.3 A) using the map to model in Phenix 1.18.2.3874, with a DNA sequence input in fasta format and the map as a .ccp4 file. However the output model fitted in the map I am getting is many fragmented PDB files and only one chain of DNA. What is the best way to get a higher fraction of the DNA model fitted into the map, can I switch off the segmentation of map and get both strands fitted into the map. Or the only option is to manually build? Thanks for your help Regards Manoj Saxena

2 2

Model moving out of map
by Shanti Pal Gangwar 03 Aug '20

03 Aug '20

Dear all, I am trying to refine a Cryo-EM map at a decent resolution. The model was fit into the map in chimera and refined against the same map in Real space refinement in Phenix but after the run, a significant part of the model moved out of the density. I would appreciate any suggestion/strategy to solve this issue. Thank you Shanti Pal

2 1

Postdoc position at UT Health Science Center, San Antonio, Texas
by Yogesh Gupta 02 Aug '20

02 Aug '20

The laboratory of Dr. Yogesh Gupta at University of Texas Health Science Center in San Antonio is seeking an enthusiastic Postdoctoral Fellow to study the structure and function of nucleoproteins in infectious diseases and cancer. We combine structural biology tools (X-ray, cryo-EM, NMR) with cell-based methods to address mechanistic questions and exploit this knowledge for drug development. Please visit below websites to learn about our research program – https://www.nature.com/articles/s41467-020-17496-8 *http://ccri.uthscsa.edu/YGupta.html <http://ccri.uthscsa.edu/YGupta.html>* Preference will be given to applicants with demonstrated experience in macromolecular crystallography. Candidates are expected to possess strong organizational, interpersonal skills, and ability to work as part of a team. An ideal candidate should hold (or soon expect to hold) a Ph.D. or equivalent degree in biochemistry/biophysics/structural biology and have no more than 2 years of postdoc experience. Salary is competitive. San Antonio offers affordable cost of living and there is no state income tax in Texas. If interested in applying, please send a short description of your research accomplishments, and CV with a list of 3 references to Dr. Yogesh Gupta (email: *guptay(a)uthscsa.edu <guptay(a)uthscsa.edu>*). The Greehey Children’s Cancer Research Institute is a unique specialized cancer research center focusing on basic and translational research in childhood cancer and occupies a state-of-the-art 100,000 sq. foot research facility on the university’s Greehey Academic and Research Campus. San Antonio is the nation’s seventh largest city and is located at the edge of the beautiful Texas Hill Country. San Antonio offers a rich, multi-cultural community, affordable cost of living, excellent weather and a thriving biomedical industry.* All Postdoctoral appointments are designated as security sensitive positions. The University of Texas Health Science Center at San Antonio is an Equal Opportunity/Affirmative Action Employer including protected veterans and persons with disabilities.* Thank you very much for your time. Yogesh -- Yogesh Gupta, PhD Assistant Professor of Biochemistry & Structural Biology PI, Greehey Children's Cancer Research Institute University of Texas Health Science Center 8403 Floyd Curl Drive, San Antonio, Texas, USA 78229 http://ccri.uthscsa.edu/YGupta.html

1 0

Fwd: Sanofi Postdoctoral Fellowship: Computational Scientist for Antibody Engineering (Greater Boston, MA)
by yanfeng zhou 31 Jul '20

31 Jul '20

If you have strong interest in one of the following areas, please continue to read and check the link for more details. 1. Developing new algorithms to revolutionize biologics discovery 2. Challenging yourself with large and unique datasets and converting your learnings to tools/products that can help patients 3. Engineering of antibody, nanobody, and other biotherapeutics modalities 4. Learning how scientists from various training backgrounds collaborate together to discover and deliver faster and better biologics treatments. The Protein Engineering group within Sanofi Large Molecule Research Department is seeking a highly talented Computational Scientist for a postdoctoral position. We use leading-edge structural biology and computational tools to support biologics project needs from Sanofi’s multi-targeting, multi-modality research pipeline. Our team has a great track record of patents and publications, including Science, Nature Cancer, and Nature Communications, in the area of biologics characterization, antibody engineering and multi-specific antibodies. This postdoc project will focus on developing a machine learning approach to predict epitope-paratope, given any antibody-antigen pair, by combining in-depth understanding of structure biology, antibody engineering, and large datasets both internally and externally. The successful candidate will be with Ph. D. degree in related area and has an advanced understanding and practical experience with developing and applying complex machine learning solutions for structural biology data. The successful candidate will gain deeper insight into drug development process and transform AI/ML algorithms into accelerating biologics discovery and development process. Application Link: https://sanofi.wd3.myworkdayjobs.com/en-US/StudentPrograms/job/Framingham-M… *About Sanofi:* Every day, Sanofi's 100,000 employees are committed to improve the lives of people around the world, with sustainable and responsible solutions and initiatives. Sanofi is recognized as one of the leading biopharmaceutical companies in the world and is pioneering innovation in biologics with the first approved nanobody drug, the first clinical stage tri-specific antibody, and a novel genetic codon expansion platform for new engineering capabilities. Details of the organization and the company’s mission and goals can be found on our website (http://www.sanofi.us/l/us/en/index.jsp). ------------------------------ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 -- Yanfeng Zhou, Ph.D. Email: YanfengZhou.pku(a)gmail.com <yanfengzhou.pku(a)gmail.com>

1 1

postdoctoral position at the Institute for Protein Innovation in Boston, USA
by Christopher Bahl 29 Jul '20

29 Jul '20

The Bahl Lab <http://function-structure.org/> at the Institute for Protein Innovation (IPI) in Boston is recruiting Postdoctoral Fellows. We use protein design to accelerate drug discovery and to engineer new lead therapeutic molecules. In addition to traditional academic collaborations, we work closely with pharmaceutical and biotech companies, as well as venture capital firms. We are looking for translationally-minded scientists who want their work to have a direct impact on the world. We will provide training in computational protein design using Rosetta, including de novo protein design and the design of protein function and biophysical properties. Postdoctoral Fellows at IPI leverage our high-throughput automated laboratory infrastructure. We are especially excited to expand our work in the following research areas: - prediction and design of protein developability for therapeutic applications - engineering of de novo miniprotein/peptide lead therapeutics for oncology, infectious disease, hypertension and diabetes, etc. - antibody design, including de novo paratope design - enzyme design Strong candidates will have demonstrated expertise in one or more of the following: - protein biochemistry: protein production and biophysical characterization, enzymology - structural biology: cryo-EM, X-ray crystallography, NMR - immuno-oncology: cell culture models, fluorescence activated cell sorting - traditional protein engineering: directed evolution, library construction, yeast and/or phage display - computational biology: machine learning, data science, molecular dynamics and/or modeling If you are excited to join a team of protein designers working to tackle audacious projects aimed directly at improving human health, please send your CV to: chris.bahl(a)proteininnovation.org About IPI The Institute for Protein Innovation is a non-profit organization that is advancing protein science to accelerate research and improve human health. The Institute is located at Harvard Medical School. IPI uniquely combines the freedom of academic exploration with the high-throughput scaling of industry to take on transformative protein-based initiatives that no other laboratory or organization can or will pursue. IPI is deploying state-of-the-art technologies to build a repository of powerful protein tools and reagents and share them through licensing and collaboration. These will enable new biomedical and therapeutic discovery for researchers in academia and industry alike. This constellation of vanguard technology and expertise positions IPI to train the next generation of entrepreneurs and protein scientists to lead the discovery of new medicines. The IPI is an equal opportunity employer and prohibits discrimination based on ethnicity, religion, sexual orientation, gender identity/expression, national origin/ancestry, age, disability, socioeconomic status, marital or veteran status, etc. Candidates from underrepresented backgrounds are especially encouraged to apply. -- PLEASE NOTE: This message, including any attachments, may include privileged, confidential and/or inside information belonging to IPI. Any distribution or use of this communication by anyone other than the intended recipient(s) is strictly prohibited and may be unlawful. If you are not the intended recipient, please notify the sender by replying to this message and then delete it from your system. Thank you.

1 0

Re: [phenixbb] Phaser-MR output after each component placement
by Randy Read 28 Jul '20

28 Jul '20

Hi Boaz, At the moment, that is indeed the only thing you can do with the partial solution information from the log file. In the CCP4 environment, you can cut and paste lines from the log file to make a .sol file, and use that to run something like a refinement job to produce a PDB and MTZ for a partial solution, but the Phenix environment uses Python pickle files to store the transformations, so that option doesn’t apply. (Unless you run Phaser from a script, in which case the Phenix and CCP4 versions work the same.) At one point, Phaser was writing out a PDB file for the top solution at every point in the process, but we felt that led to clutter and that it was confusing. There’s a major rewrite going on at the moment, and the new phasertng will primarily be run through the phaser.voyager pipeline. One of the design criteria here was to be able to examine branches that weren’t taken or intermediate points in the ongoing search, and to be able to work with them while the overall job is still running. So there will be a better option in the hopefully not too distant future! Best wishes, Randy ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > On 27 Jul 2020, at 23:02, Boaz Shaanan <bshaanan(a)bgu.ac.il> wrote: > > Hi, > The closest option that comes to mind to do what you're looking for is to take the Euler angles+translations for each of the monomers in the .sol file (or at the top of the final pdb file) and apply each of them to the initial model using any transformation program of your choice. > I am more familiar with running Phaser using the ccp4 gui but it shouldn't be very different under Phenix. > Phaser people may well suggest a more elegant option. > Stay safe, > Boaz > > Boaz Shaanan, Ph.D. > Department of Life Sciences > Ben Gurion University of the Negev > Beer Sheva > Israel > > On Jul 27, 2020 16:02, Johannes Cramer <johannes.cramer(a)gmail.com> wrote: > Dear phenix board, > > does anyone of you know if there is an option in phaser-MR to output a pdb after each placed component? > For example: I suspect there to be 5 molecules in the AU. I start a replacement with 5 molecules and phaser places 1 (I would like to inspect that), 2 (again, I would like to look at the e.g. top 10 results), 3 and so on... > Is that possible? I couldn't find the option in the gui or in the phenix documentation, but maybe in the CLI? > I know I can run one after the other, but that would potentially waste CPU time until I find time to inspect them. > > Cheers, > Johannes > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

2 1

Visiting Research Specialist Position at the University of Illinois to Study Ribosome Structure
by Yury Polikanov 27 Jul '20

27 Jul '20

The Polikanov Laboratory at the University of Illinois at Chicago (IL, USA) is looking for a talented, skillful, and highly motivated researcher to fill the *Visiting Research Specialist* position to study the structure and function of the bacterial ribosome. The research in the Polikanov Laboratory is focused on understanding the basic principles of protein synthesis in bacteria, the modes of action of ribosome-targeting antibiotics, and the mechanisms of drug resistance at a structural level. More information about Dr. Polikanov's research can be obtained from the most recent publications ( https://www.ncbi.nlm.nih.gov/sites/myncbi/yury.polikanov.1/bibliography/503…) or found on the laboratory web-page ( https://bios.uic.edu/bios/people/faculty/yury-polikanov). The successful candidate will be involved in the determination of high-resolution structures of ribosome functional complexes with various protein translation factors, tRNAs, and antibiotics using macromolecular X-ray crystallography and potentially cryo-EM techniques. *Basic qualifications:* - BS degree in chemistry, biochemistry, biophysics, or a related field; - MS degree or higher is preferred; - Minimum 3 years of laboratory research experience; - Strong background in biochemistry and molecular biology; - Practical skills with the most standard methods currently used in molecular biology, and biochemistry (such as protein expression, purification); - Experience in structural biology (cryo-EM or X-ray crystallography) is desired; - Experience in RNA biology is desired. *The successful candidate is also expected to:* - Act independently in terms of planning and executing the experiments; - Compile, analyze, and prepare data for publications; - Assist with training of graduate and undergraduate students. For fullest consideration, please submit an application and cover letter describing your scientific interests and how your previous research accomplishments and scientific interests fit with the scope of the research in the Polikanov research group at https://jobs.uic.edu/job-board/job-details?jobID=133847 by August 14, 2020. The University of Illinois at Chicago is an Equal Opportunity, Affirmative Action employer. Minorities, women, veterans, and individuals with disabilities are encouraged to apply. The University of Illinois may conduct background checks on all job candidates upon acceptance of a contingent offer. Background checks will be performed in compliance with the Fair Credit Reporting Act.

1 0